Rohingya refugees get some rest in a stadium in Aceh, Indonesia on Wednesday. The UN’s refugee body said that between January and March this year, almost 25,000 Rohingya and Bangladeshis boarded smugglers’ boats.
Photograph: Jun Ha/EPA

Malaysia said on Wednesday it would no longer accept new arrivals of ethnic minority Rohingya fleeing persecution in Burma, as the UN refugee agency expressed surprise that south-east Asian nations were now turning back boats.

Up to 8,000 impoverished Bangladeshi migrants and Rohingya asylum seekers are still believed to be stranded at sea close to Malaysia and Indonesia.

Nearly 2,000 were rescued from abandoned people-smuggling boats in the two countries at the weekend.

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One vessel that reached Indonesian waters early on Monday was turned away by the country’s navy after being given supplies and directions to Malaysia.

Malaysia’s deputy home minister, Wan Junaidi Tuanku Jaafar, however, said his country would use tough measures, including turning back asylum-seeker boats and deportation in order to send the “right message”.

“We don’t want them to come here,” the deputy minister said. His ministry oversees the police and immigration agencies.

“We are not prepared to accept that number coming into our shores and those people who are already in, we are sending them home anyway.

“I would like them to be turned back and ask them to go back to their own country. We cannot tell them we are welcoming them.”

He said Malaysia would only consider rescuing asylum seekers on humanitarian grounds if their boats had capsized. He added that a meeting will be convened soon involving Burma and Bangladeshi embassy officials to discuss how to send the migrants back.

His statement signals a change in stance for authorities in Muslim-majority Malaysia, which in the past quietly tolerated the arrival of Rohingya, a persecuted Muslim minority in predominantly Buddhist Burma.

For many Rohingyas, relatively affluent Malaysia came to be seen as one of the last safe havens in a region where many countries have been cracking down on boat people in recent years.

Rohingya asylum seekeers in Malaysia were given documents issued by the UN refugee agency, acknowledging their need to be protected, although the country is not a signatory to the UN refugee convention. While they are not officially allowed to work, authorities turn a blind eye to those working in the informal sector.

International groups have expressed concerned at the south-east Asian nations’ decision to turn away migrant boats, a controversial practice that has been used by Australia against immigrants seeking to reach its shores and has sparked heated debate.

“UNHCR is surprised at reports of Indonesia turning back one of the boats,” its Bangkok-based regional spokeswoman Vivian Tan said. “Such a practice is inconsistent with Indonesia’s search-and-rescue efforts to date, which have focused on saving lives.

“We continue to appeal to countries in the region to share responsibility and avert a humanitarian crisis.”

Some of the estimated 8,000 Bangladeshi and Rohingya boat people have been on the perilous sea journey since early March and are in urgent need of medical treatment to save their lives, International Organisation for Migration Asia-Pacific spokesman Joe Lowry said.

The 1,158 migrants who are held on Malaysia’s Langkawi island appeared “hungry and tired” when they were rescued, according to Langkawi police chief Harith Kam Abdullah.

He said they face deportation once the immigration authorities complete their investigation, and that Malaysia is stepping up sea patrols along its borders “to prevent any further illegal encroachment into Malaysian waters”.

The sudden jump in the number of migrants stuck at sea comes after Thailand cracked down on people-smuggling networks following the grim discovery of mass graves along the Thai-Malaysia border, a traditional route for the Rohingya.

About 25,000 Bangladeshis and Rohingya boarded rickety smugglers’ boats in the first three months of this year, almost double the number in the same period of 2014, according to a UNHCR report released last week.